From 0bf8b0ec36fa7c2723020852c10e6aa74a04e04a Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@ucsd.edu>
Date: Sun, 2 Mar 2025 09:39:16 -0800
Subject: [PATCH 1/4] Document NL_SINGLE_FLAG

---
 html/src/cgyro/cgyro_list.rst  | 22 ++++++++++++++++++++++
 html/src/cgyro/cgyro_table.rst |  1 +
 2 files changed, 23 insertions(+)

diff --git a/html/src/cgyro/cgyro_list.rst b/html/src/cgyro/cgyro_list.rst
index 5aa1d14..9a0fe8e 100644
--- a/html/src/cgyro/cgyro_list.rst
+++ b/html/src/cgyro/cgyro_list.rst
@@ -840,6 +840,28 @@ Toggle inclusion of nonlinear terms.
   
 ----
 
+.. _cgyro_nl_single_flag:
+
+NL_SINGLE_FLAG
+--------------
+
+**Definition**
+
+Toggle FP precision used by nonlinear terms compute.
+
+**Choices**
+
+- NL_SINGLE_FLAG=0: Use full FP64 (double) precision for all phases, including compute and MPI communication.
+- NL_SINGLE_FLAG=1: Use FP64 (double) precision for foreard communication and compute, FP32 (single) precision for reverse communication.
+- NL_SINGLE_FLAG=2: Use FP32 (single) precision for all phases, including compute and MPI communication.
+
+**Comments**
+
+- DEFAULT = 0
+- Use of FP32 validated for modest sized simulations.
+  
+----
+
 .. _cgyro_n_field:
 
 N_FIELD
diff --git a/html/src/cgyro/cgyro_table.rst b/html/src/cgyro/cgyro_table.rst
index cfd9f62..dc599fa 100644
--- a/html/src/cgyro/cgyro_table.rst
+++ b/html/src/cgyro/cgyro_table.rst
@@ -196,6 +196,7 @@ Tabular list for input.cgyro
    :widths: 13, 25, 5
 
    ":ref:`cgyro_toroidals_per_proc`", How many toroidal harmonics per MPI process,1
+   ":ref:`cgyro_nl_single_flag`", Use FP64 or FP32 math for nonlinear term,1
    ":ref:`cgyro_mpi_rank_order`", Relative ordering of MPI ranks,2
    ":ref:`cgyro_velocity_order`", What internal velocity order to use,1
    ":ref:`cgyro_gpu_bigmem_flag`", Enable GPU offload when possible, 1

From e76e95d9be79eb04e59730e6f50475bd804d7e4e Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@ucsd.edu>
Date: Sun, 2 Mar 2025 09:47:05 -0800
Subject: [PATCH 2/4] Fix defaults

---
 html/src/cgyro/cgyro_table.rst | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/html/src/cgyro/cgyro_table.rst b/html/src/cgyro/cgyro_table.rst
index dc599fa..ebc1aef 100644
--- a/html/src/cgyro/cgyro_table.rst
+++ b/html/src/cgyro/cgyro_table.rst
@@ -97,6 +97,7 @@ Tabular list for input.cgyro
    ":ref:`cgyro_n_xi`", Number of pitch angle :math:`\xi` gridpoints,16
    ":ref:`cgyro_n_energy`", Number of energy :math:`u` gridpoints,8
    ":ref:`cgyro_e_max`", Maximum energy ,8.0
+   ":ref:`cgyro_nl_single_flag`", Use FP64 or FP32 math for nonlinear term,0
 
 .. _tab-dissipation:
 
@@ -196,7 +197,8 @@ Tabular list for input.cgyro
    :widths: 13, 25, 5
 
    ":ref:`cgyro_toroidals_per_proc`", How many toroidal harmonics per MPI process,1
-   ":ref:`cgyro_nl_single_flag`", Use FP64 or FP32 math for nonlinear term,1
+   ":ref:`cgyro_collision_precision_mode`", Use FP64 or FP32 constants for the cmat constants,0
+   ":ref:`cgyro_nl_single_flag`", Use FP64 or FP32 math for nonlinear term,0
    ":ref:`cgyro_mpi_rank_order`", Relative ordering of MPI ranks,2
    ":ref:`cgyro_velocity_order`", What internal velocity order to use,1
    ":ref:`cgyro_gpu_bigmem_flag`", Enable GPU offload when possible, 1

From f7e934779bf0051f5efbfb5d469126725b0e07aa Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@ucsd.edu>
Date: Sun, 2 Mar 2025 10:16:45 -0800
Subject: [PATCH 3/4] Add conda build instructions

---
 html/src/build.rst           | 12 +++++++++---
 html/src/build/pre_conda.rst | 23 +++++++++++++++++++++++
 2 files changed, 32 insertions(+), 3 deletions(-)
 create mode 100644 html/src/build/pre_conda.rst

diff --git a/html/src/build.rst b/html/src/build.rst
index f89639d..bb9270f 100644
--- a/html/src/build.rst
+++ b/html/src/build.rst
@@ -8,6 +8,7 @@ You will need suitable python and fortran environments. There is detailed help f
 
 * :doc:`OSX users <build/pre_osx>` (MAC M2)
 * :doc:`Linux users <build/pre_linux>` (MINT, UBUNTU)
+* :doc:`Conda users, works on both OSX and Linux <build/pre_conda>` (CONDA_OMPI_GNU)
 
 If you need more help, please raise an issue at https://github.com/gafusion/gacode/issues
 
@@ -21,11 +22,11 @@ You should clone the gacode repository from GitHub. This was you can keep you in
 Concept of platform files
 -------------------------
 
-In order to compile the full GACODE package on a new machine, **platform files** must be created. You can use existing ones or create your own.  After cloning the repository, you can query the existing platforms using::
+In order to compile the full GACODE package on a new machine, a version of the **platform files** must be selected. You can use existing ones or create your own.  After cloning the repository, you can query the existing platforms using::
 
   $ ./gacode/shared/bin/gacode_platforms 
 
-To create new platform files (say, for a new platform MINE) then copy/edit the following files::
+If you decide to create new platform files (say, for a new platform MINE) then create the following files, starting from one of the existing ones (say, CONDA_OMPI_GNU)::
 
   $GACODE_ROOT/platform/build/make.inc.MINE
   $GACODE_ROOT/platform/exec/exec.MINE
@@ -46,7 +47,7 @@ To use your new platform files, enter the following lines in your shell RC file:
 OpenBLAS
 --------
 
-When building with gfortran, we recommend using `OpenBLAS <https://github.com/xianyi/OpenBLAS.git>`_. It is important to build with **single-threaded** settings. In the Makefile.rule file in the top-level OpenBLAS directory, set::
+Using system provided builds is better, but when building from scrath with gfortran, we recommend using `OpenBLAS <https://github.com/xianyi/OpenBLAS.git>`_. It is important to build with **single-threaded** settings. In the Makefile.rule file in the top-level OpenBLAS directory, set::
 
    BINARY=64
    USE_THREAD=0
@@ -68,6 +69,11 @@ To build the entire GACODE project, type::
 
   $ cd $GACODE_ROOT ; make
 
+To build just one of the tools, go into the specific subdirectory::
+
+  $ cd $GACODE_ROOT/cgyro ; make
+
+
 To test that the build is successful, you can run regression tests::
 
   $ neo -r
diff --git a/html/src/build/pre_conda.rst b/html/src/build/pre_conda.rst
new file mode 100644
index 0000000..1debf52
--- /dev/null
+++ b/html/src/build/pre_conda.rst
@@ -0,0 +1,23 @@
+Conda setup
+-----------
+
+The conda setup can be used as a regular user (no sudo privileges needed), and works on both OSX and Linux.
+
+If you do not have an existing conda setup yet, download and install Miniconda from https://www.anaconda.com/download/
+
+
+Once inside the conda setup, create the conda gacode environment.
+
+On Linux::
+
+  $ conda create -n gacode -c conda-forge gfortran binutils make python fftw openmpi netcdf4 libopenblas=*=*openmp*
+
+On OSX::
+
+  $ conda create -n gacode -c conda-forge gfortran make python fftw openmpi netcdf4
+
+
+Since many conda environment can co-exist on a single machine, activate the gacode one when using the GACODE tools::
+
+  $ conda activate gacode
+

From 896970e926e95f785fc81ffb19e86192ad27be49 Mon Sep 17 00:00:00 2001
From: Igor Sfiligoi <isfiligoi@ucsd.edu>
Date: Sun, 2 Mar 2025 10:26:08 -0800
Subject: [PATCH 4/4] Rebuild html files

---
 docs/.buildinfo                 |   4 +-
 docs/README.html                |  22 ++---
 docs/build.html                 |  33 +++++---
 docs/build/pre_conda.html       | 143 ++++++++++++++++++++++++++++++++
 docs/build/pre_linux.html       |  22 ++---
 docs/build/pre_osx.html         |  22 ++---
 docs/cgyro.html                 |  36 ++++----
 docs/cgyro/FAQ.html             |  24 +++---
 docs/cgyro/cgyro_list.html      |  41 ++++++---
 docs/cgyro/cgyro_table.html     |  36 +++++---
 docs/cgyro/outputs.html         |  24 +++---
 docs/cgyro/running_cases.html   |  25 +++---
 docs/genindex.html              |  22 ++---
 docs/geometry.html              |  36 ++++----
 docs/gyro.html                  |  26 +++---
 docs/gyro/gyro_gallery.html     |  34 ++++----
 docs/gyro/gyro_history.html     |  24 +++---
 docs/gyro/gyro_list.html        |  24 +++---
 docs/gyro/gyro_table.html       |  22 ++---
 docs/gyro/gyro_vv.html          |  42 +++++-----
 docs/index.html                 |  26 +++---
 docs/input_gacode.html          |  24 +++---
 docs/misc.html                  |  23 ++---
 docs/neo.html                   |  24 +++---
 docs/neo/neo_list.html          |  24 +++---
 docs/neo/neo_table.html         |  24 +++---
 docs/neo/outputs.html           |  24 +++---
 docs/objects.inv                | Bin 11022 -> 11065 bytes
 docs/prgen.html                 |  22 ++---
 docs/rotation.html              |  24 +++---
 docs/search.html                |  22 ++---
 docs/searchindex.js             |   2 +-
 docs/setup.html                 |  22 ++---
 docs/shortfall.html             |  42 +++++-----
 docs/tglf.html                  |  24 +++---
 docs/tglf/tglf_list.html        |  24 +++---
 docs/tglf/tglf_output_list.html |  24 +++---
 docs/tglf/tglf_table.html       |  24 +++---
 docs/tgyro.html                 |  23 ++---
 docs/tgyro/equations.html       |  24 +++---
 docs/tgyro/output.html          |  22 ++---
 docs/tgyro/plot.html            |  22 ++---
 docs/tgyro/scenarios.html       |  24 +++---
 docs/tgyro/solver.html          |  24 +++---
 docs/tgyro/tgyro_list.html      |  24 +++---
 docs/tgyro/tgyro_table.html     |  24 +++---
 docs/workshop.html              |  22 ++---
 docs/zreferences.html           |  22 ++---
 48 files changed, 767 insertions(+), 525 deletions(-)
 create mode 100644 docs/build/pre_conda.html

diff --git a/docs/.buildinfo b/docs/.buildinfo
index 740e5b1..63226e7 100644
--- a/docs/.buildinfo
+++ b/docs/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
-# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 42f11e50cbc4f08b64c4600c66d325f5
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 2e9c92f25ca4f7071953c982cc4cb35f
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/README.html b/docs/README.html
index 64c7704..db3cb49 100644
--- a/docs/README.html
+++ b/docs/README.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Using GACODE &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
-      <script src="_static/jquery.js?v=5d32c60e"></script>
-      <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
diff --git a/docs/build.html b/docs/build.html
index 4f08060..7bdef57 100644
--- a/docs/build.html
+++ b/docs/build.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Build on your laptop &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
-      <script src="_static/jquery.js?v=5d32c60e"></script>
-      <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -109,6 +111,7 @@ <h2>First step<a class="headerlink" href="#first-step" title="Link to this headi
 <ul class="simple">
 <li><p><a class="reference internal" href="build/pre_osx.html"><span class="doc">OSX users</span></a> (MAC M2)</p></li>
 <li><p><a class="reference internal" href="build/pre_linux.html"><span class="doc">Linux users</span></a> (MINT, UBUNTU)</p></li>
+<li><p><a class="reference internal" href="build/pre_conda.html"><span class="doc">Conda users, works on both OSX and Linux</span></a> (CONDA_OMPI_GNU)</p></li>
 </ul>
 <p>If you need more help, please raise an issue at <a class="reference external" href="https://github.com/gafusion/gacode/issues">https://github.com/gafusion/gacode/issues</a></p>
 </section>
@@ -121,11 +124,11 @@ <h2>Source code<a class="headerlink" href="#source-code" title="Link to this hea
 </section>
 <section id="concept-of-platform-files">
 <h2>Concept of platform files<a class="headerlink" href="#concept-of-platform-files" title="Link to this heading"></a></h2>
-<p>In order to compile the full GACODE package on a new machine, <strong>platform files</strong> must be created. You can use existing ones or create your own.  After cloning the repository, you can query the existing platforms using:</p>
+<p>In order to compile the full GACODE package on a new machine, a version of the <strong>platform files</strong> must be selected. You can use existing ones or create your own.  After cloning the repository, you can query the existing platforms using:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ ./gacode/shared/bin/gacode_platforms
 </pre></div>
 </div>
-<p>To create new platform files (say, for a new platform MINE) then copy/edit the following files:</p>
+<p>If you decide to create new platform files (say, for a new platform MINE) then create the following files, starting from one of the existing ones (say, CONDA_OMPI_GNU):</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$GACODE_ROOT/platform/build/make.inc.MINE
 $GACODE_ROOT/platform/exec/exec.MINE
 $GACODE_ROOT/platform/env/env.MINE (if needed)
@@ -145,7 +148,7 @@ <h2>Environment variables<a class="headerlink" href="#environment-variables" tit
 </section>
 <section id="openblas">
 <h2>OpenBLAS<a class="headerlink" href="#openblas" title="Link to this heading"></a></h2>
-<p>When building with gfortran, we recommend using <a class="reference external" href="https://github.com/xianyi/OpenBLAS.git">OpenBLAS</a>. It is important to build with <strong>single-threaded</strong> settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:</p>
+<p>Using system provided builds is better, but when building from scrath with gfortran, we recommend using <a class="reference external" href="https://github.com/xianyi/OpenBLAS.git">OpenBLAS</a>. It is important to build with <strong>single-threaded</strong> settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">BINARY</span><span class="o">=</span><span class="mi">64</span>
 <span class="n">USE_THREAD</span><span class="o">=</span><span class="mi">0</span>
 <span class="n">USE_LOCKING</span><span class="o">=</span><span class="mi">1</span>
@@ -167,6 +170,10 @@ <h2>Building<a class="headerlink" href="#building" title="Link to this heading">
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd $GACODE_ROOT ; make
 </pre></div>
 </div>
+<p>To build just one of the tools, go into the specific subdirectory:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd $GACODE_ROOT/cgyro ; make
+</pre></div>
+</div>
 <p>To test that the build is successful, you can run regression tests:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ neo -r
 $ tglf -r
diff --git a/docs/build/pre_conda.html b/docs/build/pre_conda.html
new file mode 100644
index 0000000..1830f16
--- /dev/null
+++ b/docs/build/pre_conda.html
@@ -0,0 +1,143 @@
+<!DOCTYPE html>
+<html class="writer-html5" lang="en" data-content_root="../">
+<head>
+  <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
+
+  <meta name="viewport" content="width=device-width, initial-scale=1.0" />
+  <title>Conda setup &mdash; GACODE</title>
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
+
+  
+    <link rel="shortcut icon" href="../_static/favicon.ico"/>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+    <script src="../_static/js/theme.js"></script>
+    <link rel="index" title="Index" href="../genindex.html" />
+    <link rel="search" title="Search" href="../search.html" /> 
+</head>
+
+<body class="wy-body-for-nav"> 
+  <div class="wy-grid-for-nav">
+    <nav data-toggle="wy-nav-shift" class="wy-nav-side">
+      <div class="wy-side-scroll">
+        <div class="wy-side-nav-search" >
+
+          
+          
+          <a href="../index.html" class="icon icon-home">
+            GACODE
+          </a>
+<div role="search">
+  <form id="rtd-search-form" class="wy-form" action="../search.html" method="get">
+    <input type="text" name="q" placeholder="Search docs" aria-label="Search docs" />
+    <input type="hidden" name="check_keywords" value="yes" />
+    <input type="hidden" name="area" value="default" />
+  </form>
+</div>
+        </div><div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="Navigation menu">
+              <p class="caption" role="heading"><span class="caption-text">Software</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../README.html">Using GACODE</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../setup.html">Prebuilt Environments</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../build.html">Build on your laptop</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../zreferences.html">References</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Codes</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../neo.html">NEO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tgyro.html">TGYRO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../cgyro.html">CGYRO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../gyro.html">GYRO</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../tglf.html">TGLF</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../prgen.html">profiles_gen</a></li>
+</ul>
+<p class="caption" role="heading"><span class="caption-text">Physics</span></p>
+<ul>
+<li class="toctree-l1"><a class="reference internal" href="../geometry.html">FLUX-SURFACE GEOMETRY</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../rotation.html">PLASMA ROTATION THEORY</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../input_gacode.html">input.gacode</a></li>
+<li class="toctree-l1"><a class="reference internal" href="../misc.html">Miscellaneous</a></li>
+</ul>
+
+        </div>
+      </div>
+    </nav>
+
+    <section data-toggle="wy-nav-shift" class="wy-nav-content-wrap"><nav class="wy-nav-top" aria-label="Mobile navigation menu" >
+          <i data-toggle="wy-nav-top" class="fa fa-bars"></i>
+          <a href="../index.html">GACODE</a>
+      </nav>
+
+      <div class="wy-nav-content">
+        <div class="rst-content">
+          <div role="navigation" aria-label="Page navigation">
+  <ul class="wy-breadcrumbs">
+      <li><a href="../index.html" class="icon icon-home" aria-label="Home"></a></li>
+      <li class="breadcrumb-item active">Conda setup</li>
+      <li class="wy-breadcrumbs-aside">
+            <a href="../_sources/build/pre_conda.rst.txt" rel="nofollow"> View page source</a>
+      </li>
+  </ul>
+  <hr/>
+</div>
+          <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+           <div itemprop="articleBody">
+             
+  <section id="conda-setup">
+<h1>Conda setup<a class="headerlink" href="#conda-setup" title="Link to this heading"></a></h1>
+<p>The conda setup can be used as a regular user (no sudo privileges needed), and works on both OSX and Linux.</p>
+<p>If you do not have an existing conda setup yet, download and install Miniconda from <a class="reference external" href="https://www.anaconda.com/download/">https://www.anaconda.com/download/</a></p>
+<p>Once inside the conda setup, create the conda gacode environment.</p>
+<p>On Linux:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda create -n gacode -c conda-forge gfortran binutils make python fftw openmpi netcdf4 libopenblas=*=*openmp*
+</pre></div>
+</div>
+<p>On OSX:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda create -n gacode -c conda-forge gfortran make python fftw openmpi netcdf4
+</pre></div>
+</div>
+<p>Since many conda environment can co-exist on a single machine, activate the gacode one when using the GACODE tools:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda activate gacode
+</pre></div>
+</div>
+</section>
+
+
+           </div>
+          </div>
+          <footer>
+
+  <hr/>
+
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+    <p>&#169; Copyright 2010-2025.</p>
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diff --git a/docs/build/pre_linux.html b/docs/build/pre_linux.html
index 8f283dc..34d7601 100644
--- a/docs/build/pre_linux.html
+++ b/docs/build/pre_linux.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Ubuntu/Mint &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
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diff --git a/docs/build/pre_osx.html b/docs/build/pre_osx.html
index 6a14389..e558275 100644
--- a/docs/build/pre_osx.html
+++ b/docs/build/pre_osx.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>OSX Sonoma &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
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-      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="../_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
diff --git a/docs/cgyro.html b/docs/cgyro.html
index c247e9d..737178c 100644
--- a/docs/cgyro.html
+++ b/docs/cgyro.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>CGYRO &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
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-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
-      <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -120,14 +122,10 @@ <h2>Brief description<a class="headerlink" href="#brief-description" title="Link
 <section id="simulation-images">
 <h2>Simulation images<a class="headerlink" href="#simulation-images" title="Link to this heading"></a></h2>
 <p>Simulation data courtesy Nathan Howard (MIT)</p>
-<a class="reference internal image-reference" href="_images/b250.png"><img alt="b250" src="_images/b250.png" style="width: 48%;" />
-</a>
-<a class="reference internal image-reference" href="_images/b990.png"><img alt="b990" src="_images/b990.png" style="width: 48%;" />
-</a>
-<a class="reference internal image-reference" href="_images/b1020.png"><img alt="b1020" src="_images/b1020.png" style="width: 48%;" />
-</a>
-<a class="reference internal image-reference" href="_images/b1480.png"><img alt="b1480" src="_images/b1480.png" style="width: 48%;" />
-</a>
+<a class="reference internal image-reference" href="_images/b250.png"><img alt="b250" src="_images/b250.png" style="width: 48%;" /></a>
+<a class="reference internal image-reference" href="_images/b990.png"><img alt="b990" src="_images/b990.png" style="width: 48%;" /></a>
+<a class="reference internal image-reference" href="_images/b1020.png"><img alt="b1020" src="_images/b1020.png" style="width: 48%;" /></a>
+<a class="reference internal image-reference" href="_images/b1480.png"><img alt="b1480" src="_images/b1480.png" style="width: 48%;" /></a>
 </section>
 <section id="cgyro-source-code">
 <h2>CGYRO Source Code<a class="headerlink" href="#cgyro-source-code" title="Link to this heading"></a></h2>
diff --git a/docs/cgyro/FAQ.html b/docs/cgyro/FAQ.html
index d10a66c..71d29e8 100644
--- a/docs/cgyro/FAQ.html
+++ b/docs/cgyro/FAQ.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>FAQ &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
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diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html
index ca48bf5..b6a20c6 100644
--- a/docs/cgyro/cgyro_list.html
+++ b/docs/cgyro/cgyro_list.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Alphabetical list for input.cgyro &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
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-      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="../_static/contentui.js"></script>
-      <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -695,6 +697,23 @@ <h1>Alphabetical list for input.cgyro<a class="headerlink" href="#alphabetical-l
 </ul>
 <hr class="docutils" />
 </section>
+<section id="nl-single-flag">
+<span id="cgyro-nl-single-flag"></span><h2>NL_SINGLE_FLAG<a class="headerlink" href="#nl-single-flag" title="Link to this heading"></a></h2>
+<p><strong>Definition</strong></p>
+<p>Toggle FP precision used by nonlinear terms compute.</p>
+<p><strong>Choices</strong></p>
+<ul class="simple">
+<li><p>NL_SINGLE_FLAG=0: Use full FP64 (double) precision for all phases, including compute and MPI communication.</p></li>
+<li><p>NL_SINGLE_FLAG=1: Use FP64 (double) precision for foreard communication and compute, FP32 (single) precision for reverse communication.</p></li>
+<li><p>NL_SINGLE_FLAG=2: Use FP32 (single) precision for all phases, including compute and MPI communication.</p></li>
+</ul>
+<p><strong>Comments</strong></p>
+<ul class="simple">
+<li><p>DEFAULT = 0</p></li>
+<li><p>Use of FP32 validated for modest sized simulations.</p></li>
+</ul>
+<hr class="docutils" />
+</section>
 <section id="n-field">
 <span id="cgyro-n-field"></span><h2>N_FIELD<a class="headerlink" href="#n-field" title="Link to this heading"></a></h2>
 <p><strong>Definition</strong></p>
diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html
index d21b574..2035976 100644
--- a/docs/cgyro/cgyro_table.html
+++ b/docs/cgyro/cgyro_table.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Tabular list for input.cgyro &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
-      <script src="../_static/jquery.js?v=5d32c60e"></script>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="../_static/doctools.js?v=9bcbadda"></script>
-      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="../_static/contentui.js"></script>
-      <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -379,6 +381,10 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 <td><p>Maximum energy</p></td>
 <td><p>8.0</p></td>
 </tr>
+<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-nl-single-flag"><span class="std std-ref">NL_SINGLE_FLAG</span></a></p></td>
+<td><p>Use FP64 or FP32 math for nonlinear term</p></td>
+<td><p>0</p></td>
+</tr>
 </tbody>
 </table>
 <span id="tab-dissipation"></span><table class="docutils align-default" id="id6">
@@ -679,6 +685,14 @@ <h1>Tabular list for input.cgyro<a class="headerlink" href="#tabular-list-for-in
 <td><p>How many toroidal harmonics per MPI process</p></td>
 <td><p>1</p></td>
 </tr>
+<tr class="row-odd"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-collision-precision-mode"><span class="std std-ref">COLLISION_PRECISION_MODE</span></a></p></td>
+<td><p>Use FP64 or FP32 constants for the cmat constants</p></td>
+<td><p>0</p></td>
+</tr>
+<tr class="row-even"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-nl-single-flag"><span class="std std-ref">NL_SINGLE_FLAG</span></a></p></td>
+<td><p>Use FP64 or FP32 math for nonlinear term</p></td>
+<td><p>0</p></td>
+</tr>
 <tr class="row-odd"><td><p><a class="reference internal" href="cgyro_list.html#cgyro-mpi-rank-order"><span class="std std-ref">MPI_RANK_ORDER</span></a></p></td>
 <td><p>Relative ordering of MPI ranks</p></td>
 <td><p>2</p></td>
diff --git a/docs/cgyro/outputs.html b/docs/cgyro/outputs.html
index a8af15c..a8bf49f 100644
--- a/docs/cgyro/outputs.html
+++ b/docs/cgyro/outputs.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>CGYRO output files &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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     <link rel="index" title="Index" href="../genindex.html" />
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diff --git a/docs/cgyro/running_cases.html b/docs/cgyro/running_cases.html
index d89579c..04cac54 100644
--- a/docs/cgyro/running_cases.html
+++ b/docs/cgyro/running_cases.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Running Cases &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="../_static/doctools.js?v=9bcbadda"></script>
-      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="../_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 
@@ -102,8 +104,7 @@ <h2>Quick-start example<a class="headerlink" href="#quick-start-example" title="
 </pre></div>
 </div>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/out.cgyro.ball.png"><img alt="Ballooning mode" src="../_images/out.cgyro.ball.png" style="width: 90%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/out.cgyro.ball.png"><img alt="Ballooning mode" src="../_images/out.cgyro.ball.png" style="width: 90%;" /></a>
 </figure>
 </section>
 <section id="command-line-usage">
diff --git a/docs/genindex.html b/docs/genindex.html
index 5dad3de..f602633 100644
--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -1,23 +1,25 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
   <meta charset="utf-8" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Index &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
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+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 
diff --git a/docs/geometry.html b/docs/geometry.html
index 3fd1015..7953bd8 100644
--- a/docs/geometry.html
+++ b/docs/geometry.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>FLUX-SURFACE GEOMETRY &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
-      <script src="_static/jquery.js?v=5d32c60e"></script>
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-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
-      <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -194,8 +196,7 @@ <h2>Equilibria<a class="headerlink" href="#equilibria" title="Link to this headi
 <li><p>For experimental profiles, shape parameters are auto-generated from profile data.</p></li>
 </ul>
 <figure class="align-center">
-<a class="reference internal image-reference" href="_images/mxh.png"><img alt="Shape moments" src="_images/mxh.png" style="width: 90%;" />
-</a>
+<a class="reference internal image-reference" href="_images/mxh.png"><img alt="Shape moments" src="_images/mxh.png" style="width: 90%;" /></a>
 </figure>
 </section>
 <section id="table-of-geometry-parameters">
@@ -358,12 +359,10 @@ <h2>Table of geometry parameters<a class="headerlink" href="#table-of-geometry-p
 <h2>Magnetic field orientation<a class="headerlink" href="#magnetic-field-orientation" title="Link to this heading"></a></h2>
 <p>GACODE uses a right-handed (positively-oriented), field-aligned coordinate system <span class="math notranslate nohighlight">\((r,\theta,\varphi)\)</span>, whereas DIII-D uses a (positively-oriented) cylindrical system <span class="math notranslate nohighlight">\((R,\phi,Z)\)</span>.  Looking down on the tokamak from above, the orientation of the GACODE toroidal angle is clockwise, whereas the DIII-D toroidal angle is counter-clockwise:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="_images/Orient_gacode.png"><img alt="flux surface" src="_images/Orient_gacode.png" style="width: 600.0px; height: 600.0px;" />
-</a>
+<a class="reference internal image-reference" href="_images/Orient_gacode.png"><img alt="flux surface" src="_images/Orient_gacode.png" style="width: 600.0px; height: 600.0px;" /></a>
 </figure>
 <figure class="align-center">
-<a class="reference internal image-reference" href="_images/Orient_d3d.png"><img alt="flux surface" src="_images/Orient_d3d.png" style="width: 600.0px; height: 600.0px;" />
-</a>
+<a class="reference internal image-reference" href="_images/Orient_d3d.png"><img alt="flux surface" src="_images/Orient_d3d.png" style="width: 600.0px; height: 600.0px;" /></a>
 </figure>
 <p>In reality, quantities like the safety factor and poloidal flux have definite signs. Historically, these signs have been suppressed or neglected in both theory and modeling. For proper treatment of momentum transport, however, these signs must be retained. We can infer typically neglected signs by knowing <a class="reference internal" href="cgyro/cgyro_list.html#cgyro-ipccw"><span class="std std-ref">IPCCW</span></a> and <a class="reference internal" href="cgyro/cgyro_list.html#cgyro-btccw"><span class="std std-ref">BTCCW</span></a>. For example:</p>
 <ul class="simple">
@@ -374,8 +373,7 @@ <h2>Magnetic field orientation<a class="headerlink" href="#magnetic-field-orient
 </ul>
 <p>The standard configuration in DIII-D is shown below.</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="_images/Orient_d3d_standard.png"><img alt="flux surface" src="_images/Orient_d3d_standard.png" style="width: 600.0px; height: 600.0px;" />
-</a>
+<a class="reference internal image-reference" href="_images/Orient_d3d_standard.png"><img alt="flux surface" src="_images/Orient_d3d_standard.png" style="width: 600.0px; height: 600.0px;" /></a>
 </figure>
 <p>This corresponds to <a class="reference internal" href="cgyro/cgyro_list.html#cgyro-ipccw"><span class="std std-ref">IPCCW</span></a> = 1 and <a class="reference internal" href="cgyro/cgyro_list.html#cgyro-btccw"><span class="std std-ref">BTCCW</span></a> =-1.  Thus, in GACODE coordinates, we expect:</p>
 <ul class="simple">
diff --git a/docs/gyro.html b/docs/gyro.html
index 27b744a..5a0529f 100644
--- a/docs/gyro.html
+++ b/docs/gyro.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>GYRO &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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     <link rel="shortcut icon" href="_static/favicon.ico"/>
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-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -106,8 +109,7 @@
              
   <section id="gyro">
 <h1>GYRO<a class="headerlink" href="#gyro" title="Link to this heading"></a></h1>
-<a class="reference internal image-reference" href="_images/supertorus-hi-2.jpg"><img alt="Classic GYRO torus" src="_images/supertorus-hi-2.jpg" style="width: 95%;" />
-</a>
+<a class="reference internal image-reference" href="_images/supertorus-hi-2.jpg"><img alt="Classic GYRO torus" src="_images/supertorus-hi-2.jpg" style="width: 95%;" /></a>
 <section id="quick-links">
 <h2>Quick links<a class="headerlink" href="#quick-links" title="Link to this heading"></a></h2>
 <div class="toctree-wrapper compound">
diff --git a/docs/gyro/gyro_gallery.html b/docs/gyro/gyro_gallery.html
index c8c1b23..9a13378 100644
--- a/docs/gyro/gyro_gallery.html
+++ b/docs/gyro/gyro_gallery.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Gallery of classic GYRO images (circa 2003) &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
-      <script src="../_static/jquery.js?v=5d32c60e"></script>
-      <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="../_static/doctools.js?v=9bcbadda"></script>
-      <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="../_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />
@@ -108,20 +110,16 @@
   <section id="gallery-of-classic-gyro-images-circa-2003">
 <h1>Gallery of classic GYRO images (circa 2003)<a class="headerlink" href="#gallery-of-classic-gyro-images-circa-2003" title="Link to this heading"></a></h1>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/supertorus-hi-1.jpg"><img alt="High resolution torus, linear phase" src="../_images/supertorus-hi-1.jpg" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/supertorus-hi-1.jpg"><img alt="High resolution torus, linear phase" src="../_images/supertorus-hi-1.jpg" style="width: 75%;" /></a>
 </figure>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/supertorus-hi-2.jpg"><img alt="High resolution torus, nonlinear phase" src="../_images/supertorus-hi-2.jpg" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/supertorus-hi-2.jpg"><img alt="High resolution torus, nonlinear phase" src="../_images/supertorus-hi-2.jpg" style="width: 75%;" /></a>
 </figure>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/candy-torus-1.jpg"><img alt="Close-up torus, linear phase" src="../_images/candy-torus-1.jpg" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/candy-torus-1.jpg"><img alt="Close-up torus, linear phase" src="../_images/candy-torus-1.jpg" style="width: 75%;" /></a>
 </figure>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/candy-torus-2.jpg"><img alt="Close-up torus, nonlinear phase" src="../_images/candy-torus-2.jpg" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/candy-torus-2.jpg"><img alt="Close-up torus, nonlinear phase" src="../_images/candy-torus-2.jpg" style="width: 75%;" /></a>
 </figure>
 <p>To use these figures in a presentation or publication, please include attribution <em>Figures courtesy J. Candy and R. Waltz, General Atomics</em> and the image URL.</p>
 </section>
diff --git a/docs/gyro/gyro_history.html b/docs/gyro/gyro_history.html
index b1d19e1..668ec1d 100644
--- a/docs/gyro/gyro_history.html
+++ b/docs/gyro/gyro_history.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Gyrokinetic Simulation in the 2000s &mdash; GACODE</title>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
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+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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+        <script src="../_static/doctools.js?v=9a2dae69"></script>
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diff --git a/docs/gyro/gyro_list.html b/docs/gyro/gyro_list.html
index 702cb30..483c7d9 100644
--- a/docs/gyro/gyro_list.html
+++ b/docs/gyro/gyro_list.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
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@@ -7,19 +5,23 @@
 
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diff --git a/docs/gyro/gyro_table.html b/docs/gyro/gyro_table.html
index ec511c2..479d636 100644
--- a/docs/gyro/gyro_table.html
+++ b/docs/gyro/gyro_table.html
@@ -1,5 +1,3 @@
-
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@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Tabular list for input.gyro &mdash; GACODE</title>
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diff --git a/docs/gyro/gyro_vv.html b/docs/gyro/gyro_vv.html
index bc9b162..f9d8b91 100644
--- a/docs/gyro/gyro_vv.html
+++ b/docs/gyro/gyro_vv.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>GYRO verification and validation (pre 2010) &mdash; GACODE</title>
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@@ -121,8 +123,7 @@ <h3>Cyclone Base Case with Adiabatic Electrons (2001)<a class="headerlink" href=
 <p>A complete <span class="math notranslate nohighlight">\(R/L_T\)</span> scan for the Cyclone Base Case with adiabatic electron
 was published in <span id="id1">[<a class="reference internal" href="../zreferences.html#id30" title="J. Candy and R.E. Waltz. An Eulerian gyrokinetic-Maxwell solver. J. Comput. Phys., 186:545, 2003. doi:doi.org/10.1016/S0021-9991(03)00079-2.">CW03a</a>]</span>.  We reproduce below Fig. 11 from that publication:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/candy_jcp2003_fig11.png"><img alt="candy_jcp2003_fig11" src="../_images/candy_jcp2003_fig11.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/candy_jcp2003_fig11.png"><img alt="candy_jcp2003_fig11" src="../_images/candy_jcp2003_fig11.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 1:</strong> <span class="math notranslate nohighlight">\(\chi_i\)</span> versus <span class="math notranslate nohighlight">\(R/L_T\)</span> scan for the Cyclone Base Case, compared with results from the LLNL and Univ. of Colorado gyrokinetic PIC codes.</p>
 </section>
@@ -130,8 +131,7 @@ <h3>Cyclone Base Case with Adiabatic Electrons (2001)<a class="headerlink" href=
 <h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-limit-of-global-simulations-2004" title="Link to this heading"></a></h3>
 <p>After the publication of this work, a community-wide benchmark exercise was carried out between codes with local capability (GYRO and GS2) and a global code (GTC).  The difficulties encountered by the global code in attempting to reproduce the local limit in <span class="math notranslate nohighlight">\(s-\alpha\)</span> geometry was addressed in <span id="id2">[<a class="reference internal" href="../zreferences.html#id33" title="J. Candy, R.E. Waltz, and W. Dorland. The local limit of global gyrokinetic simulations. Phys. Plasmas, 11:L25, 2004. doi:doi.org/10.1063/1.1695358.">CWD04</a>]</span>, where it was demonstrated that the local limit can be achieved in a truly global simulation.  We reproduce below Fig. 3 of that paper:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/candy_pop2004_fig3.png"><img alt="candy_pop2004_fig3" src="../_images/candy_pop2004_fig3.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/candy_pop2004_fig3.png"><img alt="candy_pop2004_fig3" src="../_images/candy_pop2004_fig3.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 2:</strong> Curves show radial profile of <span class="math notranslate nohighlight">\(\chi_i\)</span> averaged over the time inteval <span class="math notranslate nohighlight">\(400 \le (c_s/a) t \le 900\)</span>, as computed by GYRO.  Solid dots show results of three separate GS2 flux-tube simulations.</p>
 </section>
@@ -139,8 +139,7 @@ <h3>Local limit of Global Simulations (2004)<a class="headerlink" href="#local-l
 <h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyrokinetic-simulation-of-impurities-2004" title="Link to this heading"></a></h3>
 <p>Prior to 2004, basically all simulation work was done with pure plasmas.  As part of a Ph.D. thesis (Estrada-Mila), a paper on the topic of transport in impure plasmas <span id="id3">[<a class="reference internal" href="../zreferences.html#id61" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Gyrokinetic simulations of ion and impurity transport. Phys. Plasmas, 12:022305, 2005.">EMCW05</a>]</span> was published.  This work contained crucial benchmarks with the GS2 code.  Figure 1 from that paper is reproduced below:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/estrada_pop2005_fig1.png"><img alt="estrada_pop2005_fig1" src="../_images/estrada_pop2005_fig1.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/estrada_pop2005_fig1.png"><img alt="estrada_pop2005_fig1" src="../_images/estrada_pop2005_fig1.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 3:</strong> Adiabatic electron comparison of growth rates for the GYRO (solid line) and GS2 (black dot) codes.  Also shown are published results by Dong <span id="id4">[<a class="reference internal" href="../zreferences.html#id56" title="J.Q. Dong and W. Horton. Study of impurity mode and ion temperature gradient mode in toroidal plasmas. Phys. Plasmas, 2:3412, 1995.">DH95</a>]</span> (dotted line) which neglect trapping.  Plot (a) shows the growth rate as functions of <span class="math notranslate nohighlight">\(k_\theta \rho_s\)</span>. Plot (b) shows the effect of carbon concentration, <span class="math notranslate nohighlight">\(f_C = z_C n_C/n_e\)</span>, for <span class="math notranslate nohighlight">\(k_\theta \rho_s = 1/\sqrt{2}\)</span> and <span class="math notranslate nohighlight">\(s=1\)</span>.  All other parameters are the same in both plots.  Agreement between GYRO and GS2 is extremely good.</p>
 </section>
@@ -148,8 +147,7 @@ <h3>Gyrokinetic Simulation of Impurities (2004)<a class="headerlink" href="#gyro
 <h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#electron-temperature-gradient-turbulence-2006" title="Link to this heading"></a></h3>
 <p>Motivated by incorrect published results from a global code, a large community-wide benchmark exercise was carried out including the most advanced European gyrokinetic code, GENE.  The results were published in a paper <span id="id5">[<a class="reference internal" href="../zreferences.html#id104" title="W.M. Nevins, J. Candy, S. Cowley, T. Dannert, A. Dimits, W. Dorland, C. Estrada-Mila, G.W. Hammett, F. Jenko, M.J. Pueschel, and D.E. Shumaker. Characterizing electron temperature gradient turbulence via numerical simulation. Phys. Plasmas, 13:122306, 2006.">NCC+06</a>]</span> that clarified difficulties associated with simulations of ETG turbulence, and a new low-shear operating point was designed so that benchmark case was physically well-behaved.  Remarkable intercode agreement was obtained</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/nevins_pop2006_fig8.png"><img alt="nevins_pop2006_fig8" src="../_images/nevins_pop2006_fig8.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/nevins_pop2006_fig8.png"><img alt="nevins_pop2006_fig8" src="../_images/nevins_pop2006_fig8.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 4:</strong> <span class="math notranslate nohighlight">\(\chi_e = -Q_e/n_0 \nabla T_0\)</span> from GYRO (black curve), GS2 (blue curve), GENE (green curve), and
 PG3EQ (red curve) are plotted versus time.</p>
@@ -159,8 +157,7 @@ <h3>Electron Temperature Gradient Turbulence (2006)<a class="headerlink" href="#
 <h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="#energetic-particle-transport-coefficients-2009" title="Link to this heading"></a></h3>
 <p>Following up on initial work by Estrada-Mila <span id="id6">[<a class="reference internal" href="../zreferences.html#id62" title="C. Estrada-Mila, J. Candy, and R.E. Waltz. Density peaking and turbulent pinch in DIII-D discharges. Phys. Plasmas, 13:074505, 2006.">EMCW06a</a>]</span>, Angioni <span id="id7">[<a class="reference internal" href="../zreferences.html#id7" title="C. Angioni, A.G. Peeters, G.V. Pereverzev, A. Bottino, J. Candy, R. Dux, E. Fable, T. Hein, and R.E. Waltz. Gyrokinetic simulations of impurity, He ash and α particle transport and consequences on ITER transport modelling. Nucl. Fusion, 49:055013, 2009.">APP+09</a>]</span> carried out detailed GS2-GYRO comparsions of alpha particle quasilinear transport coefficients.  This comparison tests, among other things, the multi-scale accuracy of the gyro-averaging operators for electrons and ions.  Below we reproduce Fig. 5 of that paper:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/angioni_nf2009_fig5.png"><img alt="angioni_nf2009_fig5" src="../_images/angioni_nf2009_fig5.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/angioni_nf2009_fig5.png"><img alt="angioni_nf2009_fig5" src="../_images/angioni_nf2009_fig5.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 5:</strong> Diffusion, thermodiffusion and pure convection coefficients for <span class="math notranslate nohighlight">\(\alpha\)</span> particles in the case of a Maxwellian unperturbed distribution function, computed by linear GYRO (open squares), and linear GS2 (full circles). The codes are found in perfect agreement. The same quantities computed by GS2 in the case of an equilibrium slowing down distribution function are also plotted for comparison (full squares).  For the particle thermodiffusion coefficient <span class="math notranslate nohighlight">\(C_{T\alpha}\)</span> as well as for the diagonal heat conduction coefficient <span class="math notranslate nohighlight">\(\chi_{T\alpha}/\chi_{n\alpha}\)</span> both the actual curve obtained with a Maxwellian distribution (dashed line), as well as the same curve but rescaled by the factor <span class="math notranslate nohighlight">\(d {\rm ln} T_\alpha/d {\rm ln} T_e\)</span> (solid line), have been plotted. The latter curve allows a direct comparison with the corresponding coefficients obtained in the case of a slowing down distribution function.</p>
 </section>
@@ -168,8 +165,7 @@ <h3>Energetic particle transport coefficients (2009)<a class="headerlink" href="
 <h3>Compressional Electromagnetic Perturbations (2010)<a class="headerlink" href="#compressional-electromagnetic-perturbations-2010" title="Link to this heading"></a></h3>
 <p>Recently, compressional electromagnetic capability, <span class="math notranslate nohighlight">\(\delta B_\lVert\)</span> was added to GYRO and linear benchmarks were carried out against GS2 – the only other nonlinear code with the same capability:</p>
 <figure class="align-center">
-<a class="reference internal image-reference" href="../_images/belli_pop2010_fig1.png"><img alt="belli_pop2010_fig1" src="../_images/belli_pop2010_fig1.png" style="width: 75%;" />
-</a>
+<a class="reference internal image-reference" href="../_images/belli_pop2010_fig1.png"><img alt="belli_pop2010_fig1" src="../_images/belli_pop2010_fig1.png" style="width: 75%;" /></a>
 </figure>
 <p><strong>Figure 6:</strong> GYRO (solid red) versus GS2 (dashed red).  GYRO results without the compressional terms are shown in blue.</p>
 </section>
diff --git a/docs/index.html b/docs/index.html
index f6fdd4e..93516ce 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>The General Atomics GACODE Suite &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
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+  <!--[if lt IE 9]>
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+  
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+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
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@@ -95,8 +98,7 @@
   <section id="the-general-atomics-gacode-suite">
 <h1>The General Atomics GACODE Suite<a class="headerlink" href="#the-general-atomics-gacode-suite" title="Link to this heading"></a></h1>
 <figure class="align-center">
-<a class="reference internal image-reference" href="_images/marshall_code.png"><img alt="Marshall Rosenbluth (early 1980s)" src="_images/marshall_code.png" style="width: 90%;" />
-</a>
+<a class="reference internal image-reference" href="_images/marshall_code.png"><img alt="Marshall Rosenbluth (early 1980s)" src="_images/marshall_code.png" style="width: 90%;" /></a>
 </figure>
 <p>GACODE refers to a collection of serial and HPC software developed by the Theory Group
 at <a class="reference external" href="http://www.ga.com/magnetic-fusion">General Atomics</a>, and distributed through
diff --git a/docs/input_gacode.html b/docs/input_gacode.html
index 199930c..1b54fb2 100644
--- a/docs/input_gacode.html
+++ b/docs/input_gacode.html
@@ -1,5 +1,3 @@
-
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diff --git a/docs/misc.html b/docs/misc.html
index 100f91e..856e841 100644
--- a/docs/misc.html
+++ b/docs/misc.html
@@ -1,5 +1,3 @@
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@@ -7,18 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Miscellaneous &mdash; GACODE</title>
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diff --git a/docs/neo/neo_list.html b/docs/neo/neo_list.html
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diff --git a/docs/neo/neo_table.html b/docs/neo/neo_table.html
index ac41bcc..4593537 100644
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diff --git a/docs/neo/outputs.html b/docs/neo/outputs.html
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-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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"necessari": 14, "neo": [21, 22, 23, 24], "nersc": 27, "new_eikon": 30, "nky": 30, "nl_single_flag": 7, "nmode": 30, "nonaxisymmetr": 23, "nonlinear": 14, "nonlinear_flag": 7, "normal": [5, 9, 21], "nsts_crossphase_spectrum": 31, "nu_1": 22, "nu_e": 7, "nu_glob": 7, "numer": [8, 23], "nup_alpha": 7, "nup_radi": 7, "nup_theta": 7, "nwidth": 30, "nxgrid": 30, "omega": 27, "omega_rot": 22, "omega_rot_deriv": 22, "openbla": 1, "optim": 8, "orient": 11, "osx": 4, "out": [24, 31], "output": [5, 8, 9, 21, 24, 32, 33, 35], "overview": [12, 19, 25, 28, 29, 33], "own": 32, "p_prime_loc": 30, "parallel": 14, "paramet": [8, 11, 16, 23, 26, 32, 40], "park": 30, "particl": 17, "past": 5, "pci": 17, "perlmutt": 27, "perspect": 14, "perturb": 17, "phi": 24, "physic": [8, 18, 23, 26, 40], "plasma": [8, 18, 23, 26], "platform": 1, "plot": [5, 33, 36], "poloid": 11, "power": 34, "pre": 17, "prebuilt": 27, "prehistori": 14, "present": 28, "print_step": 7, "profil": [18, 23, 24, 26, 28, 40], "profile_dlnndr_": 22, "profile_dlntdr_": 22, "profile_equilibrium_model": 22, "profile_erad0_model": 22, "profile_model": [7, 22], "profiles_gen": 25, "public": [14, 28], "px0": 7, "python": 33, "q": [7, 22], "q_loc": 30, "q_prime_loc": 30, "q_sa": 30, "ql_flux_spectrum": 31, "quasineutral_flag": 7, "question": 5, "quick": [10, 12, 21, 29, 33], "refer": [0, 29, 42], "reflectomet": 17, "regard": 38, "relat": 8, "resolut": [8, 14, 23], "restart": 9, "restart_step": 7, "result": [17, 28], "rho_star": 22, "risk": 32, "rlns_1": 30, "rlts_1": 30, "rmaj": 7, "rmaj_loc": 30, "rmaj_over_a": 22, "rmaj_sa": 30, "rmin": 7, "rmin_loc": 30, "rmin_over_a": 22, "rmin_over_a_2": 22, "rmin_sa": 30, "rotat": [8, 18, 23, 24, 26], "rotation_model": [7, 22], "run": [5, 10, 18], "s_delta": [7, 22], "s_delta_loc": 30, "s_kappa": [7, 22], "s_kappa_loc": 30, "s_zeta": [7, 22], "s_zeta_loc": 30, "s_zmag": 22, "sat_geo_spectrum": 31, "sat_rul": 30, "satur": 29, "scalar_saturation_paramet": 31, "scenario": 37, "scienc": 14, "setup": 2, "shape": 8, "shape_cos0": [7, 22], "shape_cos1": [7, 22], "shape_cos2": [7, 22], "shape_cos3": [7, 22], "shape_s_cos0": [7, 22], "shape_s_cos1": [7, 22], "shape_s_cos2": [7, 22], "shape_s_cos3": [7, 22], "shape_s_sin3": [7, 22], "shape_sin3": [7, 22], "shat_sa": 30, "shear": 22, "shift": [7, 22], "shortfal": 28, "sign_bt": 30, "sign_it": 30, "silent_flag": [7, 22], "sim_model": 22, "simul": [5, 14, 17], "softwar": 18, "solut": [33, 38], "solv": 34, "solver": 38, "some": 38, "sonic": 26, "sonoma": 4, "sourc": [0, 1, 5, 34, 37], "space": 14, "speci": [8, 23, 24, 32, 40], "spectral": 8, "spectral_shift": 31, "spitzer_model": 22, "standard": 24, "start": 10, "step": [1, 8], "strategi": 38, "structur": 19, "studi": 17, "submiss": 10, "subroutin": [23, 24], "suit": 18, "sum_flux_spectrum": 31, "supercomput": 17, "supra": 17, "surfac": 11, "sweep": 17, "synopsi": 14, "synthet": 17, "tabl": [11, 32], "tabular": [8, 16, 40], "taus_1": 30, "te_ad": 22, "temp_": [7, 22], "temp_para_": 22, "temp_perp_": 22, "temperatur": 17, "temperature_spectrum": 31, "tglf": [29, 30, 31, 32], "tgyro": [33, 34, 38, 39, 40], "tgyro_den_method": 39, "tgyro_iteration_method": 39, "tgyro_mod": 39, "tgyro_neo_method": 39, "tgyro_relax_iter": 39, "tgyro_therm_flag": 39, "tgyro_write_profiles_flag": 39, "theoret": 26, "theori": [24, 26], "theory_nclass": 24, "theta0_sa": 30, "theta_plot": 7, "theta_trap": 30, "threed_exb_dphi0dr": 22, "threed_exb_model": 22, "threed_model": 22, "time": [8, 9], "tokamak": 17, "tore": 17, "toroid": 11, "toroidals_per_proc": 7, "toru": 14, "transport": [14, 17, 24, 33, 34], "transport_exp": 24, "transport_flux": 24, "transport_gv": 24, "turbul": 17, "ubuntu": 3, "udsymmetry_flag": 7, "ul1": 14, "ul2": 14, "ul3": 14, "ul4": 14, "unit": [30, 38], "up_alpha": 7, "up_radi": 7, "up_theta": 7, "upwind_single_flag": 7, "urban": 14, "us": 0, "usag": 10, "use_bisect": 30, "use_bp": 30, "use_bpar": 30, "use_inboard_detrap": 30, "use_mhd_rul": 30, "use_transport_model": 30, "user": 14, "valid": [17, 29], "variabl": 1, "vector": 32, "vel": 24, "vel_fouri": 24, "veloc": 14, "velocity_ord": 7, "verif": 17, "vexb": 30, "vexb_shear": 30, "vpar_1": 30, "vpar_model": 30, "vpar_shear_1": 30, "vpar_shear_model": 30, "wd_zero": 30, "width": [30, 32], "width_min": 30, "workshop": 41, "write_wavefunction_flag": 30, "xnu_factor": 30, "xnu_model": 30, "xnue": 30, "xwell_sa": 30, "yearli": 14, "your": [1, 32], "z_": [7, 22], "z_eff": 7, "z_eff_method": 7, "zeff": 30, "zeta": [7, 22], "zeta_loc": 30, "zf_test_mod": 7, "zmag": 7, "zmag_over_a": 22, "zmaj_loc": 30, "zs_1": 30}})
\ No newline at end of file
diff --git a/docs/setup.html b/docs/setup.html
index 0f30dfd..f41a4b4 100644
--- a/docs/setup.html
+++ b/docs/setup.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Prebuilt Environments &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
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       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
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-      <script src="_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
diff --git a/docs/shortfall.html b/docs/shortfall.html
index b6f890c..d44cd5a 100644
--- a/docs/shortfall.html
+++ b/docs/shortfall.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>DIII-D L-mode shortfall &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -197,8 +199,7 @@ <h2>GYRO results<a class="headerlink" href="#gyro-results" title="Link to this h
 <ul>
 <li><p>A series of linear electrostatic initial-value growth rate convergence calculations have been performed, the results of which are shown here</p>
 <figure class="align-default">
-<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.convergence.png"><img alt="linscan" src="_images/d3d128913.r8.linscan.convergence.png" style="width: 90%;" />
-</a>
+<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.convergence.png"><img alt="linscan" src="_images/d3d128913.r8.linscan.convergence.png" style="width: 90%;" /></a>
 </figure>
 </li>
 <li><p>The base case (electrostatic, finite electron-ion collisions, drift-kinetic electrons) <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a> input file can be found
@@ -220,8 +221,7 @@ <h2>GYRO results<a class="headerlink" href="#gyro-results" title="Link to this h
 </li>
 <li><p>A second set of physics tests have been done, examining the effects of using only adiabatic electrons, inclusion of ion-electron collisions, and electromagnetic effects.  These results can be seen here</p>
 <figure class="align-default">
-<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.physics.png"><img alt="linscan" src="_images/d3d128913.r8.linscan.physics.png" style="width: 90%;" />
-</a>
+<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.physics.png"><img alt="linscan" src="_images/d3d128913.r8.linscan.physics.png" style="width: 90%;" /></a>
 </figure>
 </li>
 <li><p>Text files with results for this figure can be found here:</p>
@@ -237,10 +237,8 @@ <h2>GYRO results<a class="headerlink" href="#gyro-results" title="Link to this h
 </section>
 <section id="gkw-results-added-25-jan-2013">
 <h2>GKW results (added 25-jan-2013)<a class="headerlink" href="#gkw-results-added-25-jan-2013" title="Link to this heading"></a></h2>
-<a class="reference internal image-reference" href="_images/GKW_physics_freq.png"><img alt="b250" src="_images/GKW_physics_freq.png" style="width: 48%;" />
-</a>
-<a class="reference internal image-reference" href="_images/GKW_physics_gamma.png"><img alt="b250" src="_images/GKW_physics_gamma.png" style="width: 48%;" />
-</a>
+<a class="reference internal image-reference" href="_images/GKW_physics_freq.png"><img alt="b250" src="_images/GKW_physics_freq.png" style="width: 48%;" /></a>
+<a class="reference internal image-reference" href="_images/GKW_physics_gamma.png"><img alt="b250" src="_images/GKW_physics_gamma.png" style="width: 48%;" /></a>
 <ul class="simple">
 <li><p>Text files for electrostatic <a class="reference external" href="https://bitbucket.org/gkw/gkw/wiki/Home"><cite>GKW</cite></a> electrostatic growth rates with:</p>
 <ul>
@@ -258,8 +256,7 @@ <h2>Cross-code benchmarking results<a class="headerlink" href="#cross-code-bench
 <li><p><strong>Update 27-mar-2013:</strong> Results from the gyrofluid <a class="reference internal" href="tglf.html"><span class="doc">TGLF</span></a> model have been added.</p></li>
 <li><p><strong>Update 30-may-2013:</strong> Results from the continuum gyrokinetic <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> code have been added.</p></li>
 </ul>
-<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.GYROvsGENEvsGS2vsGEMvsGKWvsTGLF.png"><img alt="b250" src="_images/d3d128913.r8.linscan.GYROvsGENEvsGS2vsGEMvsGKWvsTGLF.png" style="width: 100%;" />
-</a>
+<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.GYROvsGENEvsGS2vsGEMvsGKWvsTGLF.png"><img alt="b250" src="_images/d3d128913.r8.linscan.GYROvsGENEvsGS2vsGEMvsGKWvsTGLF.png" style="width: 100%;" /></a>
 <ul class="simple">
 <li><p>Individual code results are here for cases with finite collisions:</p>
 <ul>
@@ -273,8 +270,7 @@ <h2>Cross-code benchmarking results<a class="headerlink" href="#cross-code-bench
 </li>
 <li><p>Comparison of <a class="reference internal" href="gyro.html"><span class="doc">GYRO</span></a>, <a class="reference external" href="https://bitbucket.org/gkw/gkw/wiki/Home"><cite>GKW</cite></a>, and <a class="reference external" href="http://genecode.org"><cite>GENE</cite></a> linear calculations with no collisions and Miller geometry</p></li>
 </ul>
-<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.GYROvsGKWvsGENE_nocoll.png"><img alt="b250" src="_images/d3d128913.r8.linscan.GYROvsGKWvsGENE_nocoll.png" style="width: 100%;" />
-</a>
+<a class="reference internal image-reference" href="_images/d3d128913.r8.linscan.GYROvsGKWvsGENE_nocoll.png"><img alt="b250" src="_images/d3d128913.r8.linscan.GYROvsGKWvsGENE_nocoll.png" style="width: 100%;" /></a>
 <ul class="simple">
 <li><dl class="simple">
 <dt>Individual code results are here for cases with no collisions:</dt><dd><ul>
diff --git a/docs/tglf.html b/docs/tglf.html
index 78c0137..040b262 100644
--- a/docs/tglf.html
+++ b/docs/tglf.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>TGLF &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
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     <link rel="shortcut icon" href="_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
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diff --git a/docs/tglf/tglf_list.html b/docs/tglf/tglf_list.html
index 60c0a6d..0d1c4ff 100644
--- a/docs/tglf/tglf_list.html
+++ b/docs/tglf/tglf_list.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Alphabetical list for input.tglf &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="../_static/doctools.js?v=9bcbadda"></script>
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-      <script src="../_static/contentui.js"></script>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
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diff --git a/docs/tglf/tglf_output_list.html b/docs/tglf/tglf_output_list.html
index 4dcedce..b9331ba 100644
--- a/docs/tglf/tglf_output_list.html
+++ b/docs/tglf/tglf_output_list.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Alphabetical list for out.tglf files &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
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diff --git a/docs/tglf/tglf_table.html b/docs/tglf/tglf_table.html
index 533fa2f..af47911 100644
--- a/docs/tglf/tglf_table.html
+++ b/docs/tglf/tglf_table.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Table of inputs and outputs &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="../_static/contentui.js"></script>
+        <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
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     <link rel="index" title="Index" href="../genindex.html" />
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diff --git a/docs/tgyro.html b/docs/tgyro.html
index b038355..ef941b1 100644
--- a/docs/tgyro.html
+++ b/docs/tgyro.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>TGYRO &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
       <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
   
     <link rel="shortcut icon" href="_static/favicon.ico"/>
-      <script src="_static/jquery.js?v=5d32c60e"></script>
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-      <script src="_static/documentation_options.js?v=5929fcd5"></script>
-      <script src="_static/doctools.js?v=9bcbadda"></script>
-      <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-      <script src="_static/contentui.js"></script>
+  <!--[if lt IE 9]>
+    <script src="_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="_static/jquery.js?v=5d32c60e"></script>
+        <script src="_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="_static/doctools.js?v=9a2dae69"></script>
+        <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
+        <script src="_static/contentui.js"></script>
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diff --git a/docs/tgyro/equations.html b/docs/tgyro/equations.html
index 3db6cad..2a4bbc7 100644
--- a/docs/tgyro/equations.html
+++ b/docs/tgyro/equations.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Equations solved in TGYRO &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
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+  
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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diff --git a/docs/tgyro/output.html b/docs/tgyro/output.html
index 6842729..d3f191f 100644
--- a/docs/tgyro/output.html
+++ b/docs/tgyro/output.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>OUTPUT &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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-      <script src="../_static/documentation_options.js?v=5929fcd5"></script>
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+  <!--[if lt IE 9]>
+    <script src="../_static/js/html5shiv.min.js"></script>
+  <![endif]-->
+  
+        <script src="../_static/jquery.js?v=5d32c60e"></script>
+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
+        <script src="../_static/doctools.js?v=9a2dae69"></script>
+        <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
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diff --git a/docs/tgyro/plot.html b/docs/tgyro/plot.html
index a5aaae9..b72a536 100644
--- a/docs/tgyro/plot.html
+++ b/docs/tgyro/plot.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>PLOT &mdash; GACODE</title>
-      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=03e43079" />
-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
+      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
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     <link rel="shortcut icon" href="../_static/favicon.ico"/>
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+  <!--[if lt IE 9]>
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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diff --git a/docs/tgyro/scenarios.html b/docs/tgyro/scenarios.html
index 5db607e..9fc4a4e 100644
--- a/docs/tgyro/scenarios.html
+++ b/docs/tgyro/scenarios.html
@@ -1,5 +1,3 @@
-
-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>Scenarios and connection to energy sources &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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diff --git a/docs/tgyro/solver.html b/docs/tgyro/solver.html
index f9032b7..207d95c 100644
--- a/docs/tgyro/solver.html
+++ b/docs/tgyro/solver.html
@@ -1,5 +1,3 @@
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@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>TGYRO solver algorithm &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
+      <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
+        <script src="../_static/documentation_options.js?v=5929fcd5"></script>
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diff --git a/docs/tgyro/tgyro_list.html b/docs/tgyro/tgyro_list.html
index 5a94f81..d3b782b 100644
--- a/docs/tgyro/tgyro_list.html
+++ b/docs/tgyro/tgyro_list.html
@@ -1,5 +1,3 @@
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 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>input.tgyro Alphabetical List &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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diff --git a/docs/tgyro/tgyro_table.html b/docs/tgyro/tgyro_table.html
index e0a40d5..f39f973 100644
--- a/docs/tgyro/tgyro_table.html
+++ b/docs/tgyro/tgyro_table.html
@@ -1,5 +1,3 @@
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-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="../">
 <head>
@@ -7,19 +5,23 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>input.tgyro Tabular List &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=e59714d7" />
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+        <script src="../_static/_sphinx_javascript_frameworks_compat.js?v=2cd50e6c"></script>
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diff --git a/docs/workshop.html b/docs/workshop.html
index 74276ea..e84b63d 100644
--- a/docs/workshop.html
+++ b/docs/workshop.html
@@ -1,5 +1,3 @@
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 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>CGYRO Workshop 2022 &mdash; GACODE</title>
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-      <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
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diff --git a/docs/zreferences.html b/docs/zreferences.html
index d59f840..093d976 100644
--- a/docs/zreferences.html
+++ b/docs/zreferences.html
@@ -1,5 +1,3 @@
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-
 <!DOCTYPE html>
 <html class="writer-html5" lang="en" data-content_root="./">
 <head>
@@ -7,18 +5,22 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
   <title>References &mdash; GACODE</title>
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